Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 06:20:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/08_2023/8hgo_34744.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/08_2023/8hgo_34744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/08_2023/8hgo_34744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/08_2023/8hgo_34744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/08_2023/8hgo_34744.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/08_2023/8hgo_34744.pdb" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 109 5.16 5 C 5714 2.51 5 N 1636 2.21 5 O 1768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 531": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 9227 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4345 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 35, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 4391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4391 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 26, 'TRANS': 541} Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ASN A 182 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 182 " occ=0.00 residue: pdb=" N HIS A 183 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS A 183 " occ=0.00 residue: pdb=" N LEU A 184 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 184 " occ=0.00 residue: pdb=" N GLY A 203 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 203 " occ=0.00 residue: pdb=" N CYS A 329 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 329 " occ=0.00 residue: pdb=" N GLU A 330 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 330 " occ=0.00 residue: pdb=" N GLY A 331 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 331 " occ=0.00 residue: pdb=" N PRO A 332 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 332 " occ=0.00 residue: pdb=" N CYS A 333 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 333 " occ=0.00 Time building chain proxies: 5.07, per 1000 atoms: 0.55 Number of scatterers: 9227 At special positions: 0 Unit cell: (78.11, 131.61, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 109 16.00 O 1768 8.00 N 1636 7.00 C 5714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.02 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 523 " distance=2.04 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 539 " - pdb=" SG CYS A 555 " distance=2.04 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 42 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-3 " NAG D 2 " - " BMA D 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 801 " - " ASN A 56 " " NAG A 802 " - " ASN A 175 " " NAG D 1 " - " ASN A 352 " " NAG E 1 " - " ASN B 259 " Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.5 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 21 sheets defined 11.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.825A pdb=" N GLN B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.965A pdb=" N GLN B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 4.076A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.566A pdb=" N ASP B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.534A pdb=" N PHE B 364 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.865A pdb=" N VAL B 399 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.601A pdb=" N GLN B 426 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.063A pdb=" N GLY B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.787A pdb=" N GLY B 518 " --> pdb=" O CYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.586A pdb=" N GLN B 583 " --> pdb=" O GLU B 580 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS B 584 " --> pdb=" O ALA B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 584' Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.798A pdb=" N THR A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.746A pdb=" N GLY A 197 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 198' Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.793A pdb=" N PHE A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.934A pdb=" N LYS A 360 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.573A pdb=" N LEU A 392 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A 393 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.888A pdb=" N PHE A 420 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 421 " --> pdb=" O HIS A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 421' Processing helix chain 'A' and resid 431 through 434 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.516A pdb=" N LYS A 479 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 removed outlier: 4.427A pdb=" N CYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.743A pdb=" N CYS B 26 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.411A pdb=" N LEU B 60 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ALA B 87 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 62 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 114 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLN B 156 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL B 116 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 275 Processing sheet with id=AA5, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AA6, first strand: chain 'B' and resid 319 through 320 removed outlier: 3.695A pdb=" N GLU B 332 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 376 removed outlier: 6.440A pdb=" N LEU B 374 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 469 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AB2, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.976A pdb=" N GLN A 40 " --> pdb=" O CYS C 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.670A pdb=" N LEU A 65 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ALA A 92 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 67 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 89 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU A 122 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 91 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 119 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER A 151 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 121 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 148 " --> pdb=" O SER A 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 236 through 240 removed outlier: 3.574A pdb=" N ALA A 237 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A 250 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLY A 239 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS A 248 " --> pdb=" O GLY A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 254 through 256 removed outlier: 3.564A pdb=" N PHE A 254 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 261 " --> pdb=" O PHE A 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AB7, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AB8, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AB9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.569A pdb=" N LEU A 369 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 405 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE A 462 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A 439 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 461 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 548 through 549 removed outlier: 3.600A pdb=" N PHE A 549 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 556 " --> pdb=" O PHE A 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 38 97 hydrogen bonds defined for protein. 186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3127 1.34 - 1.46: 2001 1.46 - 1.58: 4168 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 9420 Sorted by residual: bond pdb=" C5 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.418 1.473 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C PRO B 593 " pdb=" N PRO B 594 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.51e+00 bond pdb=" C LYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.17e+00 bond pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.417 1.462 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C1 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.399 1.443 -0.044 2.00e-02 2.50e+03 4.86e+00 ... (remaining 9415 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.16: 369 107.16 - 113.87: 5176 113.87 - 120.58: 3500 120.58 - 127.29: 3628 127.29 - 134.00: 96 Bond angle restraints: 12769 Sorted by residual: angle pdb=" N LEU A 509 " pdb=" CA LEU A 509 " pdb=" C LEU A 509 " ideal model delta sigma weight residual 110.80 121.59 -10.79 2.13e+00 2.20e-01 2.57e+01 angle pdb=" N ARG A 334 " pdb=" CA ARG A 334 " pdb=" C ARG A 334 " ideal model delta sigma weight residual 110.97 115.32 -4.35 1.09e+00 8.42e-01 1.59e+01 angle pdb=" C ALA B 324 " pdb=" N GLU B 325 " pdb=" CA GLU B 325 " ideal model delta sigma weight residual 122.08 127.78 -5.70 1.47e+00 4.63e-01 1.50e+01 angle pdb=" C GLU A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 angle pdb=" N PRO B 593 " pdb=" CA PRO B 593 " pdb=" C PRO B 593 " ideal model delta sigma weight residual 110.70 114.91 -4.21 1.22e+00 6.72e-01 1.19e+01 ... (remaining 12764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 5559 18.09 - 36.18: 134 36.18 - 54.27: 60 54.27 - 72.36: 5 72.36 - 90.45: 14 Dihedral angle restraints: 5772 sinusoidal: 2390 harmonic: 3382 Sorted by residual: dihedral pdb=" CB CYS B 299 " pdb=" SG CYS B 299 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual 93.00 -176.55 -90.45 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A 219 " pdb=" SG CYS A 219 " pdb=" SG CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sinusoidal sigma weight residual 93.00 -179.51 -87.49 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 190 " pdb=" SG CYS A 190 " pdb=" SG CYS A 199 " pdb=" CB CYS A 199 " ideal model delta sinusoidal sigma weight residual -86.00 -168.44 82.44 1 1.00e+01 1.00e-02 8.34e+01 ... (remaining 5769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1224 0.076 - 0.152: 190 0.152 - 0.228: 6 0.228 - 0.304: 2 0.304 - 0.380: 3 Chirality restraints: 1425 Sorted by residual: chirality pdb=" C2 NAG A 802 " pdb=" C1 NAG A 802 " pdb=" C3 NAG A 802 " pdb=" N2 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA LEU A 509 " pdb=" N LEU A 509 " pdb=" C LEU A 509 " pdb=" CB LEU A 509 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 175 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1422 not shown) Planarity restraints: 1683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 519 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 520 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 511 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 512 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 372 " -0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO A 373 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.028 5.00e-02 4.00e+02 ... (remaining 1680 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2411 2.81 - 3.33: 7501 3.33 - 3.85: 14605 3.85 - 4.38: 16494 4.38 - 4.90: 28622 Nonbonded interactions: 69633 Sorted by model distance: nonbonded pdb=" OH TYR B 163 " pdb=" O HIS B 193 " model vdw 2.284 2.440 nonbonded pdb=" ND1 HIS A 507 " pdb=" O ALA A 508 " model vdw 2.315 2.520 nonbonded pdb=" OG SER B 38 " pdb=" OG1 THR B 41 " model vdw 2.324 2.440 nonbonded pdb=" OE2 GLU A 66 " pdb=" OH TYR A 88 " model vdw 2.349 2.440 nonbonded pdb=" O VAL B 356 " pdb=" OG SER B 380 " model vdw 2.365 2.440 ... (remaining 69628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.150 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.320 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 9420 Z= 0.239 Angle : 0.711 10.795 12769 Z= 0.397 Chirality : 0.054 0.380 1425 Planarity : 0.007 0.053 1679 Dihedral : 7.938 76.743 3457 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.03 % Favored : 91.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.20), residues: 1170 helix: -3.97 (0.38), residues: 41 sheet: -2.80 (0.49), residues: 91 loop : -2.68 (0.16), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2771 time to fit residues: 104.0993 Evaluate side-chains 229 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.0020 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 105 optimal weight: 0.0970 overall best weight: 0.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN B 438 ASN A 47 HIS A 64 ASN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 110 ASN A 158 ASN A 233 HIS A 486 GLN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN A 559 HIS A 565 GLN C 16 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 9420 Z= 0.201 Angle : 0.638 9.865 12769 Z= 0.322 Chirality : 0.047 0.270 1425 Planarity : 0.005 0.041 1679 Dihedral : 5.179 33.692 1269 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.22), residues: 1170 helix: -3.39 (0.49), residues: 63 sheet: -2.55 (0.48), residues: 104 loop : -2.26 (0.18), residues: 1003 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 256 time to evaluate : 1.084 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 258 average time/residue: 0.2723 time to fit residues: 92.5319 Evaluate side-chains 252 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 243 time to evaluate : 1.089 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1337 time to fit residues: 3.4571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 0.0970 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS B 302 ASN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 HIS B 570 GLN A 153 ASN A 233 HIS A 444 ASN A 493 ASN A 552 ASN ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9420 Z= 0.292 Angle : 0.662 9.673 12769 Z= 0.338 Chirality : 0.050 0.338 1425 Planarity : 0.005 0.043 1679 Dihedral : 5.446 28.918 1269 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.22), residues: 1170 helix: -3.41 (0.46), residues: 72 sheet: -2.28 (0.52), residues: 92 loop : -2.03 (0.18), residues: 1006 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 272 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 279 average time/residue: 0.2641 time to fit residues: 96.4787 Evaluate side-chains 261 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 248 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1143 time to fit residues: 3.9276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.0040 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 0.0010 chunk 112 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 overall best weight: 0.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS A 444 ASN A 578 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 9420 Z= 0.207 Angle : 0.635 11.299 12769 Z= 0.323 Chirality : 0.048 0.437 1425 Planarity : 0.004 0.039 1679 Dihedral : 5.386 29.814 1269 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.22), residues: 1170 helix: -2.95 (0.55), residues: 66 sheet: -2.17 (0.52), residues: 92 loop : -1.89 (0.18), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 248 time to evaluate : 1.041 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 253 average time/residue: 0.2464 time to fit residues: 83.2904 Evaluate side-chains 232 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 221 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0904 time to fit residues: 3.2455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 HIS B 470 HIS ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 9420 Z= 0.322 Angle : 0.691 9.938 12769 Z= 0.351 Chirality : 0.051 0.431 1425 Planarity : 0.005 0.041 1679 Dihedral : 5.630 28.721 1269 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.22), residues: 1170 helix: -2.95 (0.54), residues: 66 sheet: -2.18 (0.58), residues: 72 loop : -1.87 (0.18), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 250 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 257 average time/residue: 0.2596 time to fit residues: 89.4335 Evaluate side-chains 255 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 239 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1106 time to fit residues: 4.4580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 108 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 444 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 9420 Z= 0.287 Angle : 0.682 9.533 12769 Z= 0.349 Chirality : 0.050 0.398 1425 Planarity : 0.004 0.039 1679 Dihedral : 5.650 26.974 1269 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.22), residues: 1170 helix: -2.92 (0.54), residues: 66 sheet: -2.26 (0.57), residues: 72 loop : -1.82 (0.18), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 243 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 249 average time/residue: 0.2532 time to fit residues: 83.7857 Evaluate side-chains 249 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 240 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0875 time to fit residues: 2.8172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 81 optimal weight: 0.0870 chunk 94 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN B 570 GLN A 435 GLN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9420 Z= 0.273 Angle : 0.675 9.480 12769 Z= 0.345 Chirality : 0.050 0.395 1425 Planarity : 0.004 0.038 1679 Dihedral : 5.599 25.896 1269 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.23), residues: 1170 helix: -2.90 (0.53), residues: 67 sheet: -2.30 (0.59), residues: 72 loop : -1.74 (0.18), residues: 1031 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 249 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 259 average time/residue: 0.2595 time to fit residues: 89.1641 Evaluate side-chains 245 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 237 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0883 time to fit residues: 2.7247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 0.0030 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 107 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 chunk 104 optimal weight: 0.2980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN A 153 ASN A 271 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN A 559 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 9420 Z= 0.238 Angle : 0.671 9.435 12769 Z= 0.342 Chirality : 0.049 0.392 1425 Planarity : 0.004 0.038 1679 Dihedral : 5.573 23.937 1269 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.23), residues: 1170 helix: -3.19 (0.46), residues: 83 sheet: -2.59 (0.54), residues: 80 loop : -1.67 (0.19), residues: 1007 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 247 time to evaluate : 1.060 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 252 average time/residue: 0.2740 time to fit residues: 91.3019 Evaluate side-chains 247 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 241 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1548 time to fit residues: 2.9688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 94 optimal weight: 0.0870 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 9420 Z= 0.355 Angle : 0.732 9.355 12769 Z= 0.373 Chirality : 0.052 0.396 1425 Planarity : 0.005 0.052 1679 Dihedral : 5.961 26.457 1269 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.23), residues: 1170 helix: -3.17 (0.45), residues: 90 sheet: -2.62 (0.49), residues: 94 loop : -1.71 (0.19), residues: 986 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 254 time to evaluate : 1.049 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 258 average time/residue: 0.2640 time to fit residues: 89.9219 Evaluate side-chains 252 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 243 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0957 time to fit residues: 3.0405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 chunk 98 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 HIS B 530 ASN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 196 ASN A 557 GLN A 559 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 9420 Z= 0.299 Angle : 0.722 9.407 12769 Z= 0.367 Chirality : 0.051 0.389 1425 Planarity : 0.004 0.049 1679 Dihedral : 5.916 25.038 1269 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.23), residues: 1170 helix: -3.01 (0.49), residues: 80 sheet: -2.33 (0.56), residues: 80 loop : -1.67 (0.19), residues: 1010 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 1.118 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 247 average time/residue: 0.2564 time to fit residues: 83.9377 Evaluate side-chains 249 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 245 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0952 time to fit residues: 2.0891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.7676 > 50: distance: 57 - 62: 11.754 distance: 62 - 63: 10.873 distance: 63 - 64: 6.524 distance: 63 - 66: 28.701 distance: 64 - 65: 22.149 distance: 64 - 69: 6.995 distance: 66 - 67: 4.274 distance: 66 - 68: 38.435 distance: 69 - 70: 18.124 distance: 70 - 71: 6.938 distance: 70 - 73: 15.468 distance: 71 - 72: 21.206 distance: 71 - 77: 14.836 distance: 73 - 74: 20.774 distance: 73 - 75: 38.931 distance: 77 - 78: 12.402 distance: 78 - 79: 25.927 distance: 78 - 81: 28.182 distance: 79 - 80: 24.096 distance: 79 - 85: 15.613 distance: 81 - 82: 5.265 distance: 82 - 83: 26.459 distance: 82 - 84: 17.905 distance: 85 - 86: 24.900 distance: 86 - 87: 10.856 distance: 86 - 89: 11.182 distance: 87 - 88: 10.322 distance: 87 - 99: 17.695 distance: 88 - 124: 15.520 distance: 89 - 90: 9.444 distance: 90 - 91: 7.171 distance: 90 - 92: 20.115 distance: 91 - 93: 15.150 distance: 92 - 94: 27.470 distance: 92 - 95: 35.240 distance: 93 - 94: 23.131 distance: 94 - 96: 35.918 distance: 95 - 97: 14.575 distance: 96 - 98: 14.187 distance: 97 - 98: 11.114 distance: 99 - 100: 16.445 distance: 100 - 101: 11.200 distance: 100 - 103: 13.053 distance: 101 - 102: 15.215 distance: 101 - 108: 20.104 distance: 103 - 104: 5.031 distance: 104 - 105: 6.843 distance: 105 - 106: 3.957 distance: 106 - 107: 35.319 distance: 108 - 109: 16.864 distance: 109 - 110: 21.859 distance: 109 - 112: 27.551 distance: 110 - 111: 18.474 distance: 110 - 116: 14.503 distance: 112 - 113: 27.818 distance: 113 - 115: 10.559 distance: 116 - 117: 4.485 distance: 117 - 118: 21.888 distance: 117 - 120: 29.370 distance: 118 - 119: 35.471 distance: 118 - 124: 18.479 distance: 120 - 121: 12.593 distance: 120 - 122: 12.697 distance: 121 - 123: 26.168 distance: 124 - 125: 10.317 distance: 125 - 126: 34.983 distance: 125 - 128: 33.503 distance: 126 - 127: 31.185 distance: 126 - 135: 15.281 distance: 128 - 129: 10.732 distance: 129 - 130: 6.942 distance: 129 - 131: 15.472 distance: 130 - 132: 14.319 distance: 131 - 133: 4.012 distance: 132 - 134: 9.068 distance: 133 - 134: 20.245 distance: 135 - 136: 18.299 distance: 136 - 137: 30.241 distance: 136 - 139: 37.223 distance: 137 - 138: 41.372 distance: 137 - 145: 21.681 distance: 139 - 140: 5.199 distance: 140 - 141: 30.263 distance: 140 - 142: 50.265 distance: 141 - 143: 39.442 distance: 142 - 144: 40.224 distance: 143 - 144: 39.919 distance: 145 - 146: 23.607 distance: 146 - 147: 26.303 distance: 146 - 149: 41.374 distance: 147 - 148: 12.176 distance: 147 - 154: 26.123 distance: 149 - 150: 42.163 distance: 150 - 151: 17.858 distance: 151 - 152: 38.249 distance: 152 - 153: 29.157